Mutagenetix > Incidental Mutation

Incidental Mutation 'R1913:Vars2'

214627

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l

MMRRC Submission

039931-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1913 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

35655634-35667592 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 35666922 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 69 (P69S)

Ref Sequence

ENSEMBL: ENSMUSP00000047917 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001565] [ENSMUST00000043674] [ENSMUST00000160039] [ENSMUST00000160734] [ENSMUST00000160752] [ENSMUST00000162266] [ENSMUST00000165144] [ENSMUST00000169093]

AlphaFold

Q3U2A8

Predicted Effect

probably benign
Transcript: ENSMUST00000001565

SMART Domains

Protein: ENSMUSP00000001565
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	375	6.4e-141	PFAM
PDB:3DOM\|C	383	459	7e-13	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000043674
AA Change: P69S

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: P69S

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	112	736	3.3e-179	PFAM
Pfam:tRNA-synt_1g	141	221	2e-8	PFAM
Pfam:Anticodon_1	780	932	3.6e-32	PFAM
low complexity region	1005	1015	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159671

Predicted Effect

probably benign
Transcript: ENSMUST00000160039

SMART Domains

Protein: ENSMUSP00000124683
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	164	2.9e-44	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160535

Predicted Effect

probably benign
Transcript: ENSMUST00000160734

SMART Domains

Protein: ENSMUSP00000124335
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	375	1.9e-137	PFAM
PDB:3DOM\|C	383	459	7e-13	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000160752

SMART Domains

Protein: ENSMUSP00000124458
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	160	6.4e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162266

SMART Domains

Protein: ENSMUSP00000124103
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	91	1.8e-22	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162604

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162894

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162927

Predicted Effect

probably benign
Transcript: ENSMUST00000164404

SMART Domains

Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	201	1e-49	PFAM
Pfam:tRNA-synt_1g	68	172	4e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000165144
AA Change: T71I

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165787

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164978

Predicted Effect

probably benign
Transcript: ENSMUST00000168922

SMART Domains

Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	2	386	3e-105	PFAM
Pfam:Anticodon_1	430	566	8.2e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000169093

SMART Domains

Protein: ENSMUSP00000126794
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	109	1.7e-29	PFAM

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9330182L06Rik	T	G	5: 9,266,275	L2R	probably damaging	Het
Abca16	A	T	7: 120,541,240	I1588F	probably benign	Het
Abcc2	A	T	19: 43,807,244	T480S	probably benign	Het
Acnat1	A	G	4: 49,447,498	I361T	probably damaging	Het
Adamts10	A	T	17: 33,549,555	H869L	probably benign	Het
AF366264	T	A	8: 13,837,143	Q316L	probably benign	Het
Agpat5	T	C	8: 18,879,613	C253R	probably benign	Het
Agtrap	T	A	4: 148,083,977	H15L	probably damaging	Het
Ahnak	T	A	19: 9,007,922	V2190E	probably damaging	Het
Alx4	A	G	2: 93,675,387	E278G	probably damaging	Het
Amz2	T	C	11: 109,428,871	S28P	probably damaging	Het
Atr	T	A	9: 95,866,733	Y444N	probably benign	Het
Brdt	T	C	5: 107,348,613	I197T	probably benign	Het
Ccser1	G	T	6: 62,379,894	S772I	probably damaging	Het
Cdh16	T	C	8: 104,616,468	H657R	probably benign	Het
Ceacam5	A	T	7: 17,759,577	K842*	probably null	Het
Cep120	G	A	18: 53,723,286	T353I	probably benign	Het
Chrnb1	T	C	11: 69,793,584	N164S	possibly damaging	Het
Cse1l	T	C	2: 166,922,191	F123L	probably damaging	Het
Cul7	T	A	17: 46,663,190	L1467H	probably damaging	Het
Dcx	G	C	X: 143,923,103	L231V	probably damaging	Het
Dnah12	T	C	14: 26,792,264		probably null	Het
Dnah2	A	T	11: 69,464,930	M2227K	probably damaging	Het
Dnajc30	G	A	5: 135,064,332	A28T	probably benign	Het
Dnm1l	T	C	16: 16,329,966	T306A	probably benign	Het
Enpp3	C	A	10: 24,776,771	E763*	probably null	Het
Esyt3	T	C	9: 99,320,311	S516G	probably benign	Het
Exoc3	T	C	13: 74,182,316	Q498R	probably damaging	Het
Fbn2	T	A	18: 58,061,742	N1449I	probably damaging	Het
Fgb	T	C	3: 83,044,980	D194G	probably benign	Het
Fgd3	T	C	13: 49,263,848	D713G	possibly damaging	Het
Foxb1	T	A	9: 69,760,101	Y49F	possibly damaging	Het
Fpr3	A	G	17: 17,971,408	I314V	probably damaging	Het
Gfod1	A	T	13: 43,303,445	I18N	probably damaging	Het
Gm11492	T	C	11: 87,567,012	S71P	probably benign	Het
Gm5407	T	C	16: 49,296,920		noncoding transcript	Het
Gm7534	A	G	4: 134,192,675		probably null	Het
Gpr89	A	G	3: 96,875,633	F334L	possibly damaging	Het
Gucy2d	G	T	7: 98,443,847	V144F	probably benign	Het
H2-Bl	T	A	17: 36,081,016	K237M	probably damaging	Het
H2-M10.5	C	A	17: 36,774,768	P273H	probably damaging	Het
Hcn2	A	G	10: 79,730,943	M485V	probably benign	Het
Helz2	G	T	2: 181,233,750	S1650R	probably damaging	Het
Ifnar2	T	C	16: 91,404,170	V433A	probably benign	Het
Igsf21	T	A	4: 140,107,312	Y83F	probably benign	Het
Kcnk18	A	G	19: 59,235,058	I212V	possibly damaging	Het
Kcns2	T	C	15: 34,839,709	I406T	probably damaging	Het
Krt42	C	T	11: 100,267,249	V166M	possibly damaging	Het
Lama3	T	C	18: 12,495,279	M1476T	probably benign	Het
Lcor	A	G	19: 41,558,474	R166G	probably benign	Het
Mapt	C	T	11: 104,328,075	P354L	probably damaging	Het
Mep1b	A	T	18: 21,093,229	I383F	probably benign	Het
Mpzl1	C	A	1: 165,601,805	C222F	probably benign	Het
Mug2	T	C	6: 122,070,870	L780P	probably damaging	Het
Naip2	C	T	13: 100,152,157		probably null	Het
Ndufab1	T	C	7: 122,096,691	D41G	probably benign	Het
Ntn1	A	G	11: 68,213,185	C546R	probably damaging	Het
Olfr448	T	A	6: 42,896,753	F101I	probably damaging	Het
Pakap	A	G	4: 57,892,963	E880G	probably damaging	Het
Pde6b	A	G	5: 108,427,190	E639G	probably benign	Het
Phf10	T	C	17: 14,956,809	T83A	probably benign	Het
Phkb	T	A	8: 85,901,920	I186N	possibly damaging	Het
Pkhd1	A	G	1: 20,566,756		probably null	Het
Plxnd1	C	A	6: 115,978,017	A595S	possibly damaging	Het
Ppara	T	A	15: 85,801,099	H416Q	probably damaging	Het
Prodh	T	A	16: 18,081,027	D188V	probably damaging	Het
Psmd14	A	T	2: 61,785,456	K223M	possibly damaging	Het
Ptpn5	A	G	7: 47,078,868	M528T	possibly damaging	Het
Rassf9	G	A	10: 102,544,939	E59K	probably benign	Het
Rnf2	A	T	1: 151,476,185	L140H	probably damaging	Het
Scai	A	G	2: 39,080,081	F557S	probably damaging	Het
Sdk2	A	G	11: 113,856,726	S653P	possibly damaging	Het
Sec24c	A	G	14: 20,689,111	D534G	probably benign	Het
Serinc1	A	G	10: 57,519,465	V375A	probably benign	Het
Serpinb9f	C	T	13: 33,325,846	A7V	probably damaging	Het
Smco1	T	C	16: 32,273,882	S124P	probably damaging	Het
Smim23	C	A	11: 32,824,441	C26F	possibly damaging	Het
Sppl2c	T	A	11: 104,187,889	M505K	probably benign	Het
Sprr1b	C	A	3: 92,437,468	V34F	possibly damaging	Het
Sun1	G	A	5: 139,235,732		probably null	Het
Supt16	A	G	14: 52,178,135	L381P	possibly damaging	Het
Syne2	A	G	12: 75,899,246	D364G	possibly damaging	Het
Tax1bp1	G	T	6: 52,765,952	V775F	probably damaging	Het
Tial1	T	A	7: 128,444,659	I231F	probably damaging	Het
Tiam1	C	A	16: 89,798,694	V1300L	probably damaging	Het
Tmem132e	A	G	11: 82,443,417	T585A	probably damaging	Het
Tnni3k	C	T	3: 154,979,199	A165T	probably benign	Het
Tomm40	A	T	7: 19,710,961	I165N	probably damaging	Het
Tomt	T	C	7: 101,901,247	E104G	probably damaging	Het
Topaz1	T	C	9: 122,767,013	S950P	possibly damaging	Het
Traf3ip2	C	G	10: 39,625,940	P28R	probably benign	Het
Trim24	C	T	6: 37,957,815	P822S	probably damaging	Het
Upf3a	T	G	8: 13,792,108	Y175D	probably damaging	Het
Veph1	T	C	3: 66,244,555	Y151C	probably damaging	Het
Vmn2r11	T	A	5: 109,054,788	D141V	probably benign	Het
Vwa5b1	G	A	4: 138,592,020	Q442*	probably null	Het
Wdr17	T	A	8: 54,687,726	D197V	probably damaging	Het
Wdr70	G	T	15: 7,884,410	T586N	possibly damaging	Het
Wfdc18	G	A	11: 83,709,928	G52R	probably benign	Het
Zc3h6	T	C	2: 129,016,620	I857T	probably damaging	Het
Zfp318	GAAGAA	GAAGAACAAGAA	17: 46,412,524		probably benign	Het
Zfp318	TGAAGAAGAAGAAGAAGAAGAAGAAGAAG	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG	17: 46,412,514		probably benign	Het
Zfp647	C	T	15: 76,911,951	V170I	probably benign	Het
Zfp871	T	C	17: 32,775,917	N76D	possibly damaging	Het
Zwilch	A	G	9: 64,160,952	Y194H	probably damaging	Het

Other mutations in Vars2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02106:Vars2	APN	17	35664621	unclassified	probably benign
IGL02320:Vars2	APN	17	35660454	missense	probably benign	0.07
IGL02580:Vars2	APN	17	35660885	missense	possibly damaging	0.50
IGL02691:Vars2	APN	17	35660248	missense	probably damaging	1.00
IGL03039:Vars2	APN	17	35664121	missense	probably damaging	1.00
PIT4445001:Vars2	UTSW	17	35666211	nonsense	probably null
R0079:Vars2	UTSW	17	35659156	missense	probably damaging	0.99
R0152:Vars2	UTSW	17	35660027	missense	probably damaging	1.00
R0346:Vars2	UTSW	17	35664864	unclassified	probably benign
R0426:Vars2	UTSW	17	35664584	missense	probably damaging	1.00
R0584:Vars2	UTSW	17	35666686	missense	possibly damaging	0.82
R0589:Vars2	UTSW	17	35659176	missense	probably benign
R0882:Vars2	UTSW	17	35657299	missense	probably benign	0.41
R1234:Vars2	UTSW	17	35667146	missense	probably damaging	1.00
R1263:Vars2	UTSW	17	35661609	missense	probably damaging	1.00
R1559:Vars2	UTSW	17	35666258	unclassified	probably benign
R1772:Vars2	UTSW	17	35660084	missense	probably damaging	1.00
R1809:Vars2	UTSW	17	35662216	missense	probably damaging	1.00
R1986:Vars2	UTSW	17	35660061	missense	probably damaging	1.00
R2504:Vars2	UTSW	17	35664793	missense	probably damaging	1.00
R3426:Vars2	UTSW	17	35661974	missense	probably damaging	1.00
R4539:Vars2	UTSW	17	35666888	missense	probably damaging	0.99
R4751:Vars2	UTSW	17	35659343	missense	possibly damaging	0.89
R4861:Vars2	UTSW	17	35661933	missense	probably benign	0.00
R4861:Vars2	UTSW	17	35661933	missense	probably benign	0.00
R5028:Vars2	UTSW	17	35659473	critical splice donor site	probably null
R5217:Vars2	UTSW	17	35658149	missense	probably damaging	1.00
R5292:Vars2	UTSW	17	35660786	missense	probably damaging	1.00
R6056:Vars2	UTSW	17	35665788	missense	probably benign	0.01
R6211:Vars2	UTSW	17	35665662	splice site	probably null
R6213:Vars2	UTSW	17	35660440	missense	probably benign	0.27
R6374:Vars2	UTSW	17	35660045	missense	probably damaging	1.00
R6746:Vars2	UTSW	17	35660402	critical splice donor site	probably null
R6749:Vars2	UTSW	17	35666713	missense	probably damaging	1.00
R6957:Vars2	UTSW	17	35667075	missense	probably benign	0.39
R7107:Vars2	UTSW	17	35658250	missense	probably damaging	1.00
R7428:Vars2	UTSW	17	35666686	missense	probably benign	0.00
R7538:Vars2	UTSW	17	35660780	missense	probably damaging	1.00
R7553:Vars2	UTSW	17	35664788	missense	possibly damaging	0.93
R7741:Vars2	UTSW	17	35660943	missense	probably damaging	1.00
R7784:Vars2	UTSW	17	35658158	missense	possibly damaging	0.95
R7823:Vars2	UTSW	17	35659136	missense	probably damaging	1.00
R7915:Vars2	UTSW	17	35664839	missense	probably damaging	1.00
R8201:Vars2	UTSW	17	35658310	missense	probably benign
R8955:Vars2	UTSW	17	35661649	missense	probably damaging	1.00
R8964:Vars2	UTSW	17	35659807	missense	possibly damaging	0.46
R9101:Vars2	UTSW	17	35659088	missense	possibly damaging	0.51
R9202:Vars2	UTSW	17	35663552	critical splice acceptor site	probably null
R9202:Vars2	UTSW	17	35666659	missense	probably damaging	1.00
R9450:Vars2	UTSW	17	35662135	missense	probably damaging	0.98
X0021:Vars2	UTSW	17	35659034	missense	possibly damaging	0.93
Z1176:Vars2	UTSW	17	35664791	missense	possibly damaging	0.55
Z1177:Vars2	UTSW	17	35663472	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- CCAGAAACATCTGTGGAAGCAG -3'
(R):5'- CACTTTGTACACAGCCGGAG -3'

Sequencing Primer
(F):5'- GAACAGAGATCCACTACTGAACTG -3'
(R):5'- TCCCCTGTCTCTCGGAGGAAC -3'

Posted On

2014-07-14